[gmx-users] dihedral distributions

Dallas Warren Dallas.Warren at monash.edu
Fri Mar 2 03:17:42 CET 2012

1 - Those two index groups refer to two different dihedrals within your topology, and the labeling of them will come from something about the dihedral, more than likely it is from the force constant.

2 - if it starts asymmetric, then with time becomes symmetric, that may be an indicator of reaching some equilibrium.
Catch ya,

3 - you will have to look at the type of dihedral it is and the potential function it creates, then check to see if the observed distribution is consistent with that.

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Juliette N.
Sent: Friday, 2 March 2012 12:42 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dihedral distributions

Hi all,

I used the following line to obtain index file of RB dihedral quadrupltes:

mk_angndx -s *.tpr -n *-RB -type ryckaert-bellemans

The resulting index file contains two groups

[ RB-A1=1.88 ]

[ RB-A1=-1.46 ]

1- Can anyone tell me please what these groups refer to? I am not able to find the answer in the manual.

Then using g_angle -of  option  I compute dihedral fractions separately for each group. (figures attached)

g_angle -f *.trr    -n *-RB.ndx      -of    *_md-of-1.88   -b

2- The first peak of the first plot is not symmetrical as others although I collected data in the last 1 ns of a 20 ns simulation. does this mean the polymer chain has not equilibrated? this behavior is observed in the first few nanoseconds too.

3- I dont see why there are 3 peaks in the first group and 2 peaks in the [ RB-A1=-1.46 ] one?

Appreciate greatly your help,

On 1 March 2012 02:21, Mark Abraham <Mark.Abraham at anu.edu.au<mailto:Mark.Abraham at anu.edu.au>> wrote:
On 1/03/2012 5:07 PM, Juliette N. wrote:
Hi all,

Can anyone guide me how one can obtain dihedral distributions of a polymer chain and how this can be used to ensure the equilibration of system?
g_angle takes a list of dihedrals and provides the dihedral distribution of a given dihedral in the time interval -b to -e ?

Have a read of g_angle -h and try things out. You'll need to look in the literature for info on the kind of information you're looking for.


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